chr4-9993752-G-A

Variant names:

• chr4-9993752-G-A
• rs12499857
• NM_020041.3:c.410+3029C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020041.3(SLC2A9):​c.410+3029C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,678 control chromosomes in the GnomAD database, including 17,691 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.46 (17691 hom., cov: 30)
• Consequence: SLC2A9 NM_020041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 11 publications found

Genes affected

SLC2A9 (HGNC:13446): (solute carrier family 2 member 9) This gene encodes a member of the SLC2A facilitative glucose transporter family. Members of this family play a significant role in maintaining glucose homeostasis. The encoded protein may play a role in the development and survival of chondrocytes in cartilage matrices. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

SLC2A9-AS1 (HGNC:40636): (SLC2A9 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC2A9	NM_020041.3	c.410+3029C>T		intron_variant	Intron 3 of 11	ENST00000264784.8	NP_064425.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC2A9	ENST00000264784.8	c.410+3029C>T		intron_variant	Intron 3 of 11	1	NM_020041.3	ENSP00000264784.3

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69690 AN: 151560 Hom.: 17683 Cov.: 30

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.480

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.460 AC: 69710 AN: 151678 Hom.: 17691 Cov.: 30 AF XY: 0.463 AC XY: 34313 AN XY: 74108

African (AFR) AF: 0.226 AC: 9346 AN: 41350

American (AMR) AF: 0.553 AC: 8434 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1832 AN: 3470

East Asian (EAS) AF: 0.412 AC: 2113 AN: 5124

South Asian (SAS) AF: 0.590 AC: 2832 AN: 4798

European-Finnish (FIN) AF: 0.546 AC: 5735 AN: 10502

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37694 AN: 67874

Other (OTH) AF: 0.480 AC: 1008 AN: 2098

Alfa AF: 0.536 Hom.: 11726

Bravo AF: 0.450

Asia WGS AF: 0.515 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.33
PhyloP100		0.25
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12499857; hg19: chr4-9995376;